ZAP70
protein-codingzeta chain of T cell receptor associated protein kinase 70, the group of Syk family tyrosine kinases|SH2 domain containing
Gene summary
This gene encodes an enzyme belonging to the protein tyrosine kinase family, and it plays a role in T-cell development and lymphocyte activation. This enzyme, which is phosphorylated on tyrosine residues upon T-cell antigen receptor (TCR) stimulation, functions in the initial step of TCR-mediated signal transduction in combination with the Src family kinases, Lck and Fyn. This enzyme is also essential for thymocyte development. Mutations in this gene cause selective T-cell defect, a severe combined immunodeficiency disease characterized by a selective absence of CD8-positive T-cells. Two transcript variants that encode different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
- SRK
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~30.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0014861
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0010023
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0010023
Submitter: ClinGen
ZAP70 was first reported in relation to autosomal recessive combined immunodeficiency in 1994 (Arpaia E, et al., 1994, PMID: 8124727). ZAP70 related combined immunodeficiency is caused by abnormal T-cell receptor signaling with low to absent CD8+ T cells and normal CD3+ and CD4+ T cells numbers. Symptoms include recurrent infections, including severe lower respiratory infections and oral candidiasis, chronic diarrhea, and failure to thrive. Combined immunodeficiencies such as ZAP-70 deficiency or major histocompatibility complex (MHC) class I and II gene expression deficiency may not be detected with the TREC assay as T-cell development is intact beyond the point of T-cell receptor (TCR) gene recombination (PMID: 32579701). Six variants (missense, nonsense, frameshift, and splicing substitutions) that have been reported in six probands in six publications (PMIDs: 8124727, 28124082, 21094993, 30778343, 8202713, 8202712) are included in this curation. Variants in this gene segregated with disease in two additional family members (PMIDs: 27448562). Heterozygous carriers in these families did not show evidence of pathogenicity.The mechanism of pathogenicity is known to be loss of function. This gene-disease association is also supported by animal models, expression studies, biochemical studies, and functional studies in patient cells (PMIDs: 27869819, 8176201, 25092893, 25092893, 8124727). ZAP70 is expressed exclusively in T and NK cell lines and is expressed in all murine and human thymocyte subpopulations (PMID: 8176201). ZAP70 null mice have no detectable ZAP70 expression and absent T cells and when null mice with a tetracycline inducible Zap70 transgene are induced with Zap70 protein, thymocyte generation is partially restored (PMID: 25092893). ZAP70 interacts with the T cell receptor complex via its SH2 domains and is activated by Lck (PMID: 27869819). In summary, ZAP70 is definitively associated with autosomal recessive combined immunodeficiency. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. This classification was approved by the ClinGen SCID/CID GCEP on January 20, 2022 (SOP Version 8).
Inheritance Pattern: AR
Disease ID:MONDO:0010023
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0010023
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Allergy/Immunology/Infectious
Intervention: Allergy/Immunology/Infectious
Rationale: In Autoimmune disease, multisystem, infantile-onset 2, individuals may demonstrate multiple autoimmune sequelae that may be refractory to immunosuppressants, and HSCT has been described as effective; In Selective T-cell defect, prophylactic measures, in the short term, include IVIG administration as well as antiinfectious prophylaxis; If blood products are necessary, they should be irradiated and CMV and EBV-negative; Live vaccines should be avoided, and immunizations should be deferred until reconstitution of the immune system; HSCT has been described as effective in some individuals
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ZAP70 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001079.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 3 | 188 | 1 | 193 | |
| missense | 2 | 11 | 192 | 7 | 1 | 213 |
| nonsense | 9 | 2 | 2 | 13 | ||
| start loss | 1 | 1 | ||||
| frameshift | 11 | 1 | 12 | |||
| splice donor/acceptor (+/-2bp) | 1 | 5 | 6 | |||
| Total | 23 | 20 | 198 | 195 | 2 | 438 |
Highest pathogenic variant AF is 0.00002726501
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001070.2 | 12 | MANE Select | |
| Ensembl | ENSP00000264972.5 | 12 | MANE Select | |
| RefSeq | NP_001365523.1 | 12 | Standard | |
| RefSeq | NP_997402.1 | 6 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| zap70 | Danio rerio | Structure: pro-T cell Quality: decreased amount abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Primary immunodeficiency - Homo sapiens (human)
- T cell receptor signaling pathway - Homo sapiens (human)
- Th17 cell differentiation - Homo sapiens (human)
- Th1 and Th2 cell differentiation - Homo sapiens (human)
- Ras signaling pathway - Homo sapiens (human)
Biological Process
- adaptive immune response
- protein phosphorylation
- immune response
- peptidyl-tyrosine phosphorylation
- T cell differentiation
Molecular Function
- phosphotyrosine residue binding
- protein tyrosine kinase activity
- non-membrane spanning protein tyrosine kinase activity
- protein binding
- ATP binding
Cellular Component
- immunological synapse
- cytoplasm
- cytosol
- plasma membrane
- cell-cell junction
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000264972
- Coding exons
- 12
- Length
- 26303
- Individuals with no LoFs
- 125730
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 14
- Defined
- 125744
- p
- 0.0000557
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.76 | 257 | 415 | 0.619 | 0.0000300 | 4010 |
| Missense (PolyPhen) | 97 | 190.4 | 0.50945 | 1794 | ||
| Synonymous | 1.09 | 168 | 187 | 0.899 | 0.0000156 | 1186 |
| Loss of Function | 4.11 | 5 | 28.8 | 0.173 | 0.00000141 | 329 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0.00020 | 0.00020 | rare |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000056 | 0.000053 | rare |
| South Asian | 0.000067 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Tyrosine kinase that plays an essential role in regulation of the adaptive immune response. Regulates motility, adhesion and cytokine expression of mature T-cells, as well as thymocyte development. Contributes also to the development and activation of primary B-lymphocytes. When antigen presenting cells (APC) activate T-cell receptor (TCR), a serie of phosphorylations lead to the recruitment of ZAP70 to the doubly phosphorylated TCR component CD247/CD3Z through ITAM motif at the plasma membrane. This recruitment serves to localization to the stimulated TCR and to relieve its autoinhibited conformation. Release of ZAP70 active conformation is further stabilized by phosphorylation mediated by LCK. Subsequently, ZAP70 phosphorylates at least 2 essential adapter proteins: LAT and LCP2. In turn, a large number of signaling molecules are recruited and ultimately lead to lymphokine production, T-cell proliferation and differentiation. Furthermore, ZAP70 controls cytoskeleton modifications, adhesion and mobility of T-lymphocytes, thus ensuring correct delivery of effectors to the APC. ZAP70 is also required for TCR-CD247/CD3Z internalization and degradation through interaction with the E3 ubiquitin-protein ligase CBL and adapter proteins SLA and SLA2. Thus, ZAP70 regulates both T-cell activation switch on and switch off by modulating TCR expression at the T-cell surface. During thymocyte development, ZAP70 promotes survival and cell-cycle progression of developing thymocytes before positive selection (when cells are still CD4/CD8 double negative). Additionally, ZAP70-dependent signaling pathway may also contribute to primary B-cells formation and activation through B-cell receptor (BCR). {ECO:0000269|PubMed:11353765, ECO:0000269|PubMed:12051764, ECO:0000269|PubMed:1423621, ECO:0000269|PubMed:20135127, ECO:0000269|PubMed:26903241, ECO:0000269|PubMed:8124727, ECO:0000269|PubMed:8702662, ECO:0000269|PubMed:9489702}.;
- Disease
- DISEASE: Immunodeficiency 48 (IMD48) [MIM:269840]: A form of severe immunodeficiency characterized by a selective absence of CD8+ T-cells. {ECO:0000269|PubMed:11123350, ECO:0000269|PubMed:11412303, ECO:0000269|PubMed:18509675, ECO:0000269|PubMed:8124727, ECO:0000269|PubMed:8202713}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Autoimmune disease, multisystem, infantile-onset, 2 (ADMIO2) [MIM:617006]: An autosomal recessive, autoimmune disorder characterized by systemic manifestations including blistering skin disease, uncontrollable bullous pemphigoid, inflammatory colitis, autoimmune hypothyroidism, proteinuria and nephrotic syndrome. {ECO:0000269|PubMed:26783323}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.629
Intolerance Scores
- LoFtool
- 0.0533
- RVIS EVS
- -1.16
- RVIS percentile EVS
- 6.17
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.858
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |